[R-sig-eco] Quantifying functional trait diversity through Gower distance and pcoa
Phil Novack-Gottshall
pnovack-gottshall at ben.edu
Tue Nov 16 16:24:03 CET 2010
Dear Chris,
You might consider the FD library, which allows measurement of a range
of functional diversity metrics, and includes functions for Gower
distance (and, within other functions, PCoA, using, I believe, the
dudi.pco function from the ade4 library). A benefit of the library's
functions is control over the number of dimensions to include.
Laliberté, E., and B. Shipley. 2010. FD: Measuring functional diversity
(FD) from multiple traits, and other tools for functional ecology,
Version 1.0-9.
Cheers,
Phil
On 11/16/2010 9:08 AM, chris mcowen wrote:
> Dear List,
>
> I am relatively new to this area of ecology and R, coming from a
> phylogenetic background. I am looking to quantify functional trait
> diversity in in order to plot global functional trait diversity
> hotspots. My trait data are categorical and all indicies of functional
> diversity require continuous data.
>
> My approach was to generate a distance matrix based on the Gower
> method - i have done this with vegdist- and then i was planning on
> running a pcoa on these to generate the continuous data to use in the
> calculation of functional diversity indicies.
>
> I have two questions:-
>
> First, does this make sense, i appreciate i will loose information this way.
>
> Second, I have looked at vegan but can not see a way to run a pcoa on
> the output from a vegdist analysis, is this possible and once again
> does this make sense?
>
> Any help would be greatly appreciated,
>
> Chris
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
>
>
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* PLEASE NOTE NEW CONTACT INFORMATION *
Phil Novack-Gottshall
Assistant Professor
Department of Biology
Benedictine University
5700 College Road
Lisle, IL 60532
pnovack-gottshall at ben.edu
Phone: 630-829-6514
Fax: 630-829-6547
Office: 332 Birck Hall
Lab: 107 Birck Hall
http://www.ben.edu/faculty/pnovack-gottshall
* PLEASE NOTE NEW CONTACT INFORMATION *
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
More information about the R-sig-ecology
mailing list